doc: fix toctree warnings

this is done now by either including a hidden toctree
or renaming *.rst files

12 files changed, 29 insertions, 13 deletions

diff --git a/docs/source/conf.py b/docs/source/conf.py
index 24eb6a9c..dd2cccc1 100644
--- a/docs/source/conf.py
+++ b/docs/source/conf.py
@@ -93,7 +93,9 @@ release = version
 
 # List of patterns, relative to source directory, that match files and
 # directories to ignore when looking for source files.
-exclude_patterns = []
+exclude_patterns = [
+'manpage.rst'
+]
 
 # The reST default role (used for this markup: `text`) to use for all documents.
 #default_role = None
diff --git a/docs/source/configuration/accounts_table.rst b/docs/source/configuration/accounts_table
index aea1956c..aea1956c 100644
--- a/docs/source/configuration/accounts_table.rst
+++ b/docs/source/configuration/accounts_table
diff --git a/docs/source/configuration/alotrc_table.rst b/docs/source/configuration/alotrc_table
index 6b4e2092..6b4e2092 100644
--- a/docs/source/configuration/alotrc_table.rst
+++ b/docs/source/configuration/alotrc_table
diff --git a/docs/source/configuration/index.rst b/docs/source/configuration/index.rst
index 90744ef7..b14af2e1 100644
--- a/docs/source/configuration/index.rst
+++ b/docs/source/configuration/index.rst
@@ -24,7 +24,7 @@ The type of an option is used to validate a given value. For instance,
 if the type says "boolean" you may only provide "True" or "False" as values in your config file,
 otherwise alot will complain on startup. Strings *may* be quoted but do not need to be.
 
-.. include:: alotrc_table.rst
+.. include:: alotrc_table
 
 .. _account:
 
@@ -59,7 +59,7 @@ Here is an example configuration::
 
 The following entries are interpreted at the moment:
 
-.. include:: accounts_table.rst
+.. include:: accounts_table
 
 
 Contacts Completion
@@ -151,7 +151,7 @@ Hooks are python callables that live in a module specified by `hooksfile` in the
 config. Per default this points to :file:`~/.config/alot/hooks.py`.
 When a hook gets called it receives a reference to the :class:`main user interface <alot.ui.UI>` and the
 :class:`database manager <alot.db.DBManager>`.
-For every :doc:`COMMAND <../usage/commands>` in mode :ref:`MODE <modes>`, the callables :func:`pre_MODE_COMMAND` and :func:`post_MODE_COMMAND`
+For every :ref:`COMMAND <commands>` in mode :ref:`MODE <modes>`, the callables :func:`pre_MODE_COMMAND` and :func:`post_MODE_COMMAND`
 -- if defined -- will be called before and after the command is applied respectively. The signature for the
 pre-`send` hook in envelope mode for example looks like this:
 
diff --git a/docs/source/description.rst b/docs/source/description
index 9dea9693..9dea9693 100644
--- a/docs/source/description.rst
+++ b/docs/source/description
diff --git a/docs/source/generate_configs.py b/docs/source/generate_configs.py
index 123b017b..8b0009e8 100755
--- a/docs/source/generate_configs.py
+++ b/docs/source/generate_configs.py
@@ -60,9 +60,9 @@ if __name__ == "__main__":
     config = ConfigObj(None, configspec=specpath, stringify=False, list_values=False)
     config.validate(Validator())
 
-    alotrc_table_file = os.path.join(HERE, 'configuration', 'alotrc_table.rst')
+    alotrc_table_file = os.path.join(HERE, 'configuration', 'alotrc_table')
     rewrite_entries(config.configspec, alotrc_table_file, 'defaults/alot.rc.spec', sort=True)
 
-    rewrite_entries(config, os.path.join(HERE, 'configuration', 'accounts_table.rst'),
+    rewrite_entries(config, os.path.join(HERE, 'configuration', 'accounts_table'),
                     'defaults/alot.rc.spec',
                     sec=config.configspec['accounts']['__many__'])
diff --git a/docs/source/index.rst b/docs/source/index.rst
index cc227b77..4742e36d 100644
--- a/docs/source/index.rst
+++ b/docs/source/index.rst
@@ -5,7 +5,7 @@
 
 User Manual
 ===========
-.. include:: description.rst
+.. include:: description
 
 .. toctree::
    :maxdepth: 2
diff --git a/docs/source/manpage.rst b/docs/source/manpage.rst
index 0e53d82b..bfdf43da 100644
--- a/docs/source/manpage.rst
+++ b/docs/source/manpage.rst
@@ -4,16 +4,16 @@ Manpage
 Synopsis
 --------
 
-.. include:: usage/synopsis.rst
+.. include:: usage/synopsis
 
 Description
 -----------
 
-.. include:: description.rst
+.. include:: description
 
 Usage
 -----
-.. include:: usage/first_steps.rst
+.. include:: usage/first_steps
 
 
 See Also
diff --git a/docs/source/usage/commands.rst b/docs/source/usage/commands
index bc93ac1a..ec0be2eb 100644
--- a/docs/source/usage/commands.rst
+++ b/docs/source/usage/commands
@@ -1,3 +1,5 @@
+.. _commands:
+
 Commands
 ========
 
@@ -13,3 +15,15 @@ Commands
     lists all active buffers
 :doc:`modes/taglist`
     lists all tagstrings present in the notmuch database
+
+.. toctree::
+   :maxdepth: 2
+   :hidden:
+
+   modes/global
+   modes/search
+   modes/thread
+   modes/envelope
+   modes/bufferlist
+   modes/taglist
+
diff --git a/docs/source/usage/first_steps.rst b/docs/source/usage/first_steps
index e99c44ce..e99c44ce 100644
--- a/docs/source/usage/first_steps.rst
+++ b/docs/source/usage/first_steps
diff --git a/docs/source/usage/index.rst b/docs/source/usage/index.rst
index 7e97e78e..4992ba1c 100644
--- a/docs/source/usage/index.rst
+++ b/docs/source/usage/index.rst
@@ -4,11 +4,11 @@ Usage
 
 Commandline invocation
 ======================
-.. include:: synopsis.rst
+.. include:: synopsis
 
 First Steps
 ===========
 
-.. include:: first_steps.rst
+.. include:: first_steps
 
-.. include:: commands.rst
+.. include:: commands
diff --git a/docs/source/usage/synopsis.rst b/docs/source/usage/synopsis
index 5bfb8e88..5bfb8e88 100644
--- a/docs/source/usage/synopsis.rst
+++ b/docs/source/usage/synopsis